Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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 98% [==================================================] |                     done.
Writing output ct file...done.
Single strand folding complete.
Initializing nucleic acids...done.
Applying SHAPE constraints...done.
Calculating free energies...done.
efn2 complete.
Converting CT file...CT file conversion complete.
/disk1/www/rails/humanrnamap/cli/./main.py:567: DeprecationWarning: Call to deprecated function (or staticmethod) VARNA. (Class has been renamed 'Structure')
  v = VARNA(structure=fold_dbn, sequence=seq)
Output file: /disk1/www/rails/humanrnamap/public/result/de30ce64-5c9c-4402-9e9e-1db28178c1a4/final_image/MALAT1_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.97 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.97 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.97 MB
read annotations - Elapsed time since the previous call: 0.10 seconds
read annotations - Current memory usage: 172.61 MB
Based on canonical annotations, the following gene is in your area of interest: MALAT1(+)
write fasta - Elapsed time since the previous call: 0.56 seconds
write fasta - Current memory usage: 172.61 MB
Length of region: 96 nt.
100.0% of the region's A/C bases included in the filtered DMS dataset. Ideally, this number should be as high as possible for an experimenally-accurate prediction, and over 70% is recommended.
write dat - Elapsed time since the previous call: 0.22 seconds
write dat - Current memory usage: 175.85 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/de30ce64-5c9c-4402-9e9e-1db28178c1a4/fasta/MALAT1.fasta" "/disk1/www/rails/humanrnamap/public/result/de30ce64-5c9c-4402-9e9e-1db28178c1a4/ct/MALAT1.ct" --SHAPE "MALAT1.dat"

fold - Elapsed time since the previous call: 0.11 seconds
fold - Current memory usage: 175.85 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/de30ce64-5c9c-4402-9e9e-1db28178c1a4/ct/MALAT1.ct" "/disk1/www/rails/humanrnamap/public/result/de30ce64-5c9c-4402-9e9e-1db28178c1a4/fold_FE/MALAT1.txt" -sh "MALAT1.dat"

efn2 - Elapsed time since the previous call: 0.51 seconds
efn2 - Current memory usage: 175.85 MB
This region has 1 predicted structures. 5 is the maximum structures visible on the web server. For up to 20 predictions per region, download and run the code locally.
Running command: /disk1/www/rails/humanrnamap/cli/bin/ct2dot "/disk1/www/rails/humanrnamap/public/result/de30ce64-5c9c-4402-9e9e-1db28178c1a4/ct/MALAT1.ct" 1 "/disk1/www/rails/humanrnamap/public/result/de30ce64-5c9c-4402-9e9e-1db28178c1a4/fold_dbn/MALAT1_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.01 seconds
ct2dot - Current memory usage: 175.85 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CAGAUCAGGAUUUGAGCGGAAGAACGAAUGUAACUUUAAGGCAGGAAAGACAAAUUUUAUUCUUCAUAAAGUGAUGAGCAUAUAAUAAUUCCAGGC', '-structureDBN', '....(((..((((.....((((((.((((....((((........))))....))))..))))))...))))..)))...................', '-o', '/disk1/www/rails/humanrnamap/public/result/de30ce64-5c9c-4402-9e9e-1db28178c1a4/final_image/MALAT1_fold_1.svg', '-title', 'MALAT1, -4.8 ± 1.2\n kcal/mol, AUC: 0.491', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '3,5,8,9,11,12,13,14,16,18,19,22,26,29,30,31,35,36,37,40,41,44,45,49,55,56,57,58,60,61,63,64,67,71,72,73,75,76,78,81,83,86,89,90,94,95', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '2,52,7,43,93', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '1,68,69,6,70,77,20,21,92,38,39,42,46,48,53,54,59', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '65,66,4,10,74,15,79,17,80,82,84,85,23,24,25,87,27,28,88,91,32,33,34,96,47,50,51,62']
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Text: 'A', X: 189.13265163224247, Y: 139.56690662507293, Width: 10.5, Height: 8
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Text: 'C', X: 196.8281945850526, Y: 155.28405257636388, Width: 10.5, Height: 8
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Text: 'A', X: 196.8281945850526, Y: 172.7840542390132, Width: 10.5, Height: 8
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Text: 'A', X: 189.1326516322425, Y: 188.50120019030425, Width: 10.5, Height: 8
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Text: 'A', X: 175.30957045826793, Y: 199.23304462872392, Width: 10.5, Height: 8
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Text: 'U', X: 175.30957045826793, Y: 219.23304462872392, Width: 10.5, Height: 8
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Text: 'U', X: 175.30957045826793, Y: 239.23304462872392, Width: 10.5, Height: 8
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Text: 'U', X: 156.25271971898943, Y: 321.4902647451434, Width: 10.5, Height: 8
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Text: 'C', X: 147.45781115982763, Y: 339.4527140056419, Width: 10.5, Height: 8
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Text: 'U', X: 138.66290260066583, Y: 357.4151632661404, Width: 10.5, Height: 8
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Text: 'U', X: 129.86799404150403, Y: 375.37761252663887, Width: 10.5, Height: 8
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Text: 'C', X: 121.07308548234224, Y: 393.34006178713736, Width: 10.5, Height: 8
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Text: 'A', X: 128.7686252823612, Y: 409.0572074308706, Width: 10.5, Height: 8
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Text: 'U', X: 128.76862335639993, Y: 426.5572074308705, Width: 10.5, Height: 8
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Text: 'A', X: 121.07308009688248, Y: 442.27435138073923, Width: 10.5, Height: 8
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Text: 'A', X: 107.25, Y: 453.0061944952826, Width: 10.5, Height: 8
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Text: 'A', X: 107.25, Y: 473.0061944952826, Width: 10.5, Height: 8
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Text: 'G', X: 107.25, Y: 493.0061944952826, Width: 10.5, Height: 8
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Text: 'G', X: 117.62968331740177, Y: 527.0956337164137, Width: 10.5, Height: 8
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Text: 'A', X: 117.62968331740177, Y: 544.5956372402846, Width: 10.5, Height: 8
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Text: 'U', X: 107.25, Y: 558.6850764614157, Width: 10.5, Height: 8
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Text: 'G', X: 107.25, Y: 578.6850764614157, Width: 10.5, Height: 8
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Text: 'A', X: 107.25, Y: 598.6850764614157, Width: 10.5, Height: 8
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Text: 'G', X: 124.75, Y: 598.6850764614157, Width: 10.5, Height: 8
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Text: 'C', X: 142.25, Y: 598.6850764614157, Width: 10.5, Height: 8
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Text: 'A', X: 159.75, Y: 598.6850764614157, Width: 10.5, Height: 8
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Text: 'U', X: 177.25, Y: 598.6850764614157, Width: 10.5, Height: 8
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Text: 'A', X: 194.75, Y: 598.6850764614157, Width: 10.5, Height: 8
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Text: 'C', X: 369.75, Y: 598.6850764614157, Width: 10.5, Height: 8
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Text: 'G', X: 404.75, Y: 598.6850764614157, Width: 10.5, Height: 8
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Text: 'C', X: 439.75, Y: 598.6850764614157, Width: 10.5, Height: 8
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Text: '1', X: 5.5, Y: 618.6850764614157, Width: 9.0, Height: 8
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Text: '10', X: 51.2514348971348, Y: 509.84483776471666, Width: 18.0, Height: 8
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Text: '20', X: 78.9665647326955, Y: 352.29097755883913, Width: 18.0, Height: 8
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Text: '40', X: 116.6851741137053, Y: 9.502875440715115, Width: 18.0, Height: 8
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Text: '50', X: 200.89665507325336, Y: 126.94487441023915, Width: 18.0, Height: 8
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Text: '60', X: 178.59669970729283, Y: 313.5648532792065, Width: 18.0, Height: 8
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Text: '70', X: 123.5, Y: 473.0061944952826, Width: 18.0, Height: 8
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Text: '80', X: 156.0, Y: 618.6850764614157, Width: 18.0, Height: 8
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Text: '90', X: 331.0, Y: 618.6850764614157, Width: 18.0, Height: 8
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Text: '96', X: 436.0, Y: 618.6850764614157, Width: 18.0, Height: 8
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Text: 'MALAT1, -4.8 ± 1.2
 kcal/mol, AUC: 0.491', X: 156.25, Y: 631.4850764614157, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 1.5028754407151155, 454.0, 631.4850764614157)
Updated viewBox: -0.25 -3.4971245592848845 459.25 639.9822010207006
Updated SVG: /disk1/www/rails/humanrnamap/public/result/de30ce64-5c9c-4402-9e9e-1db28178c1a4/final_image/MALAT1_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/de30ce64-5c9c-4402-9e9e-1db28178c1a4/final_image/MALAT1_fold_final_1.svg
